SMTL ID : 6y90.1

Structure of full-length CD20 in complex with Rituximab Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)(Covalent)

Y01.1: 9 residues within 4Å: Chain A: S.144, L.147, G.148, S.151, F.156 Chain B: I.20, A.21, G.24 Ligands: Y01.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.20, B:A.21, A:F.156 Y01.2: 6 residues within 4Å: Chain A: I.20, G.24, M.27, L.44, H.114 Ligands: Y01.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.20, A:M.27, A:L.44, A:L.44 Y01.3: 3 residues within 4Å: Chain A: S.55, A.59 Ligands: Y01.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.59 Y01.10: 8 residues within 4Å: Chain A: K.6, I.13, M.14, L.17 Chain B: F.1, E.4, F.159 Ligands: Y01.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.13, A:L.17, B:F.159 Salt bridges: A:K.6 Y01.11: 10 residues within 4Å: Chain A: F.1, E.4, I.155, F.159 Chain B: K.6, I.13, M.14, L.17, A.59 Ligands: Y01.14 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.159, B:I.13, B:L.17 Salt bridges: B:K.6 Y01.12: 10 residues within 4Å: Chain A: I.20, A.21, I.28 Chain B: S.144, L.147, G.148, S.151, I.155, F.156 Ligands: Y01.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.155, B:F.156, A:I.28 Salt bridges: B:K.98 Y01.13: 5 residues within 4Å: Chain B: G.24, M.27, L.44, H.114 Ligands: Y01.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.44 Salt bridges: B:H.114 Y01.14: 6 residues within 4Å: Chain B: I.20, I.51, S.55, A.58, A.59 Ligands: Y01.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.20, B:I.51, B:A.59

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Covalent)

PC1.4: 6 residues within 4Å: Chain A: I.91, L.95, K.98, L.147, L.154, I.155 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.91, A:I.91, A:L.95, A:L.154, A:I.155 PC1.15: 6 residues within 4Å: Chain B: I.91, L.95, K.98, L.147, L.154, I.155 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.91, B:L.95, B:L.154, B:I.155

10 x MYS: PENTADECANE(Non-covalent)(Non-functional Binders)

MYS.5: 3 residues within 4Å: Chain A: I.88, I.91, F.102 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.88, A:I.91, A:F.102 MYS.6: 3 residues within 4Å: Chain A: S.85, L.103, M.105 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.103 MYS.7: 2 residues within 4Å: Chain A: T.39 Ligands: MYS.8 No protein-ligand interaction detected (PLIP) MYS.8: 3 residues within 4Å: Chain A: W.41, L.108 Ligands: MYS.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.41, A:L.108 MYS.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.16: 2 residues within 4Å: Chain B: I.88, F.102 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.88, B:F.102, B:F.102 MYS.17: 2 residues within 4Å: Chain B: S.85, M.105 No protein-ligand interaction detected (PLIP) MYS.18: 2 residues within 4Å: Chain B: T.39 Ligands: MYS.19 No protein-ligand interaction detected (PLIP) MYS.19: 2 residues within 4Å: Chain B: W.41 Ligands: MYS.18 No protein-ligand interaction detected (PLIP) MYS.20: 1 residues within 4Å: Chain B: L.44 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Binding mechanisms of therapeutic antibodies to human CD20. Science (2020)

Release Date

2020-08-26

Peptides

B-lymphocyte antigen CD20: AB
Rituximab Fab Heavy Chain: CE
Rituximab Fab Light Chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
H

D
D

F
L

Membrane

We predict this structure to be a membrane protein.
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B-lymphocyte antigen CD20

Rituximab Fab Heavy Chain

Rituximab Fab Light Chain

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